I can’t figure out just what you are doing or how you could be charged an extra 60,000 miles. Are you making stopovers on the way to Cusco? GP does not allow stopovers on its routings and that is stated clearly in the rules. If you stop (more than 24 hours) in Costa Rica or anywhere else and continue on to Cusco this would require two tickets. If the reservation is booked in Business Class I guess it could cost 60,000 more miles.
You said the reservations were on Taca and I assume you made it, as most of us do with the Distancia department yourself. A very big difference between Distancia and LP/GP is Distancia allows a free stopover on its routings and LP/GP does not. Unfortunately the Distancia booking people do not always know the rules for LP/GP tickets and this may be where the mistake was made. I do not know all the details so I am just speculating.
Do not get me wrong it is possible LP/GP made a mistake but without seeing your itinerary I do not know whose mistake it is. As for your friends ticket GP had to charge you the taxes when you made the reservation. They should be able to see it is a mistake and make some restitution. At the very least they should refund the taxes for a flight that was never ticketed. I believe you stated LP/GP gave you the ticket numbers to present to Distancia. If you have the two ticket numbers I am confused. If you could be more specific I am certain someone in this forum may be able to help you.
My wife and I were not always happy with the program but as we use up the last of our million miles we never regretted participating. The miles have taken us on Safari in Africa, Hilton transfers for trips to Australia. A vacation in Rome another to London. Trips to Costa Rica, Belize and Roatan; we will be using the last of our miles to go to Buenos Aires and Iguazu in December but will go back to Quito this summer. I could never complain!!!!!!!